Federal prosecutors say owner Uri Jacobson and store manager Elena Falaschetti failed to report almost $2.8 million in wages paid to employees from 2003 to 2009.
They say Wyncote-based Bare Feet Shoes employs 200 people in 12 stores in Pennsylvania and New Jersey.
They have been charged by way of an information, which can indicate a defendant's cooperation.
Defense lawyer Joseph Santaguida says he has no comment on Jacobson's behalf.
Authorities say Jacobson had Falaschetti and others falsify payroll reports. The pair are also accused of underreporting their own income.
Falaschetti's lawyer did not immediately return a call for comment.